FMO DATABASE

FMODB ID: 7651K

Calculation Name: 3S1B-A-Xray372

Preferred Name: Vascular endothelial growth factor A

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3S1B

Chain ID: A

ChEMBL ID: CHEMBL1783

UniProt ID: P15692

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	33
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-139487.037218
FMO2-HF: Nuclear repulsion	125262.712114
FMO2-HF: Total energy	-14224.325104
FMO2-MP2: Total energy	-14264.870385

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:1:PHE)

Summations of interaction energy for fragment #1(A:1:PHE)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-29.568	-18.538	2.102	-5.397	-7.735	-0.008

Interaction energy analysis for fragmet #1(A:1:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.084 / q_NPA : 0.031

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

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X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	3	LYS	1	0.927	0.939	3.406	-7.441	-3.650	0.022	-1.902	-1.911	0.010
4	A	4	GLU	-1	-0.893	-0.979	2.260	-7.379	-3.840	1.622	-2.168	-2.993	-0.010
5	A	34	CYS	0	-0.077	-0.028	2.842	-7.511	-3.915	0.459	-1.307	-2.747	-0.008
6	A	6	LEU	0	0.006	0.010	5.778	-0.668	-0.668	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.099	-0.054	6.880	-0.404	-0.404	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.986	1.006	4.845	1.562	1.562	0.000	0.000	0.000	0.000
9	A	9	TYR	0	-0.019	-0.050	8.427	-0.096	-0.096	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.871	0.939	11.540	-0.961	-0.961	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.843	-0.955	12.686	0.118	0.118	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.019	0.007	13.667	-0.067	-0.067	0.000	0.000	0.000	0.000
13	A	13	ALA	0	-0.067	-0.039	15.412	-0.036	-0.036	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.058	-0.042	16.087	0.003	0.003	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.852	-0.898	18.245	0.058	0.058	0.000	0.000	0.000	0.000
16	A	16	PRO	0	-0.053	-0.023	20.081	-0.027	-0.027	0.000	0.000	0.000	0.000
17	A	17	ASN	0	-0.035	-0.032	22.629	-0.016	-0.016	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.014	0.028	17.459	-0.033	-0.033	0.000	0.000	0.000	0.000
19	A	19	ASN	0	0.046	0.030	21.950	0.006	0.006	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.017	-0.017	22.570	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	21	TYR	0	0.037	0.018	21.648	-0.019	-0.019	0.000	0.000	0.000	0.000
22	A	22	GLN	0	-0.026	-0.038	20.432	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.979	1.001	18.107	0.001	0.001	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.027	-0.020	17.163	-0.022	-0.022	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.023	0.005	16.721	-0.050	-0.050	0.000	0.000	0.000	0.000
26	A	26	LYS	1	0.924	0.983	12.469	-0.029	-0.029	0.000	0.000	0.000	0.000
27	A	27	ILE	0	-0.027	-0.020	12.339	-0.077	-0.077	0.000	0.000	0.000	0.000
28	A	28	VAL	0	0.029	0.019	11.619	-0.106	-0.106	0.000	0.000	0.000	0.000
29	A	29	SER	0	0.022	0.013	11.025	-0.083	-0.083	0.000	0.000	0.000	0.000
30	A	30	ILE	0	-0.124	-0.065	7.348	-0.271	-0.271	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.822	-0.884	6.767	-1.262	-1.262	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.985	-0.957	7.452	-1.514	-1.514	0.000	0.000	0.000	0.000
33	A	33	ASP	-1	-0.959	-0.982	4.116	-3.230	-3.126	-0.001	-0.020	-0.084	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:PHE)